1. Laurens F., Aranzana M.J., Arus P., Bonany J., Corelli L., Durel C.E., Micheletti D.,
Patocchi A., Pascal T., Peil, A., Quilot B., Stella A., Troggio M., Troillard V., Velasco
R., van de Weg E, …
1 March 2011- 31 August 2015
EU-FP7 large collaborative project
www.fruitbreedomics.com2nd annual meeting
Lleida

2. 15
Research
1 – INRA
2 – ARO (IL)
5 – CRA-W
6 – CRA
8 – ETHZ
9 – EVD
10 – FEM
12 – IRTA
13 – JKI
15 – PTP
16 – RBIPH
18 – DLO
19 – UMIL
20 – UNIBO
21 – READING
22 – ARC (ZA)
23 – PFR (NZ)
24 – ZJU (CN)
25 – KUL
26 – RCL
SMEs
3 – ASF
4 – B3F
7 – DNV
14 – NOVADI
17 – RDG
Management
11 – IT
22
23
24
16
18
19 20
21
3
4
714
17
13
12
10
98
6
5
2
11
IsraëlNZ
China
South Africa
1
+ close links with :
Rosbreed (WSU), SLU (Sweeden)
Partners
25
+ contacts in Russia:
VNIISPK (Orel)
SKZNIISIV (Krasnodar) North
Caucasia

3. To fill in the gap between Genetics/Genomics and
breeding
- Development + use of molecular tools (SNP , Full transcript
chips) /international collaboration
- Better knowledge / genetics + genomics of major agronomic
traits + allelic diversity
 Material + tools + methodologies /breeders
AIMS

4. WP5 Trait
knowledge
WP1 Breeding/MAB WP2 Pre-BreedingEuropean Breeding
Platform
Diversity and QTL mapping
WP3 PBA
WP4 LD/GWA
WP6 SNP chips WP7 bioinfoTools
WP8Dissemination
WP9.Management
A. Patocchi (EVD) A. Peil (JKI)
E. van de Weg (DLO)
Pedigree Based Analysis
Genome Wide Association
M.J. Aranzana (IRTA)
B. Quilot (INRA)
A. Stella (PTP)R. Velasco (FEM)
V.Troillard(IT)
J.Bonani(IRTA)

5. Test the efficiency of the use of molecular markers
in current breeding programmes
WP1
Breeding/MAB

6. 1. Breeding strategies
2. Fine mapping
3. Pilot studies
4. Pipeline
5. DB interface
WP1 highlights 2012 + perspectives 2013
- Apple and peach
Questionnaires,
meetings
 priorities
- Breeding criteria
- Breeding schemes
SNP markers
tighted to most of
the targeted
genes
Selection of the
apple pilot
progenies
In progress
- Test of SNP based low cost
genotyping platforms for MAB
and GWS
- pipeline… to be discussed at the
WP1 workshop
Decision to move
towards GWS
-> MAB for MG
-> GWS for Q traits
WP1
Breeding/MAB
WP8

7. 1. Breeding strategies
2. Fine mapping
3. Pilot studies
4. Pipeline
5. DB interface
WP1 highlights 2012 + perspectives 2013
- Apple and peach
Questionnaires,
meetings
 priorities
- Breeding criteria
- Breeding schemes
SNP Markers
tighted to most of
the targeted
genes
Selection of the
apple pilot
progenies
In progress
- Test of SNP based low cost
genotyping platforms for MAB
and GWS
- pipeline… to be discussed at the
WP1 workshop
Decision to move
towards GWS
-> MAB for MG
-> GWS for Q traits
WP1
Breeding/MAB
 MAB
 GWS
On apple and
peach
Ms on fine mapping
of selected major
genes or QTLs

8. WP2
Pre-Breeding
WP2 highlights 2012 + perspectives 2013
To prepare new genitors (progenitors) for the future
breeding programmes
 Selection time

9. 1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
WP2 highlights 2012 + perspectives 2013
Plant material
evaluated for resistance
and fruit traits
New progenies created
to pyramide genes of
interest
New early apple flowering lines
carrying resistance genes (fire
blight, powdery mildew) produced
and pollinated
WP2
Pre-Breeding

10. 1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
WP2 highlights 2012 + perspectives 2013
Plant material
evaluated for resistance
and fruit traits
New progenies created
to pyramide genes of
interest
New early apple flowering lines
carrying resistance genes (fire
blight, powdery mildew) produced
and pollinated
WP2
Pre-Breeding
Phenotype and
genotype new
progenies
Put data in DB
Solve some issues
about FB early
flowering lines

11. Diversity and QTL fine
mappingWP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation Flex
WP4 LD/GA
1. Phen & genet variability
2. Core collection
3. QTL mapping by GWA
Pedigree Based Analysis
Genome Wide
Association

12. WP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation FlexPedigree Based Analysis
Peach progenies
genotyped with the 9K
IPSC SNP array
FlexQTLTM
Interface
computation time
 New functionalities
WP3 highlights 2012 + perspectives 2013
first peach QTL
mapping
analyses in
progress
Apple 20K SNP array
WP6

13. WP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation FlexPedigree Based Analysis
Peach progenies
genotyped with the 9K
IPSC SNP array
FlexQTLTM
Interface
computation time
 New functionalities
WP3 highlights 2012 + perspectives 2013
Apple 20K SNP array
Peach QTL
mapping
analyses
completed
Apple QTL mapping
analyses
Integrated
linkage map
List of EU-founders and
indications on their level of
exploitation in breeding.
(Del 3.1)
WP6
Organization of the PBA
training session
WP8

14. WP4 LD/GA
Genome Wide Association
Genetic structure of
apple and peach
germplasm.
Preliminary GWA
studies on peach
Apple and peach
phenotypic data
in FB DB
WP4 highlights 2012 + perspectives 2013
WP1
WP7
Define core collection D4.1
Test panel with
48 accessions
genotyped with
20K SNP chip
WP6

15. WP4 LD/GA
Genome Wide Association
Genetic structure of
apple and peach
germplasm.
Preliminary GWA
studies on peach
Apple and peach
phenotypic data
in FB DB
WP4 highlights 2012 + perspectives 2013
WP1
WP7
Define core collection D4.1
Test panel with
48 accessions
genotyped with
20K SNP chip
WP6
Peach GWA
studies
completed
Apple
genotyping
(choice of the
genotyping tool)
then GWA
WP6

16. WP5 Trait knowledge
1. Biotic stresses: Monilia
2. Fruit quality : texture, fiber
3. Abiotic stresses
WP5 highlights 2012 + perspectives 2013
and test of tools
and protocols
Start transcriptomics
approach
/Fruit quality

17. WP5 Trait knowledge
1. Biotic stresses: Monilia
2. Fruit quality : texture, fiber
3. Abiotic stresses
WP5 highlights 2012 + perspectives 2013
and test of tools
and protocols
Start transcriptomics
approach
/Fruit quality
Select highthrouput
phenotyping tools
Select /stop

New
tests in
2013
Analysis
of the
data

18. WP6 SNP chips Tools
Tests of low
density chips for
WP1
20k Illumina
Infinium Apple SNP
Chip available
WP6 highlights 2012 + perspectives 2013
Test apple 20k Illumina
Infinium on 48
genotypes
WP4WP1 WP3

19. WP6 SNP chips Tools
Tests of low
density chips for
WP1
20k Illumina
Infinium Apple SNP
Chip available
Selection of a genotyping
tool for apple WP4 in
progress (GBS or arrays ?)
WP6 highlights 2012 + perspectives 2013
Test apple 20k Illumina
Infinium on 48
genotypes
WP4
Protocols to be
used for large
germplasm
genotyping
WP1 WP3
WP4
WP4
Final choice = Feb
2013

20. WP7 bioinfoTools
Structure of
phenotypic DB for
apple and peach
completed
User Interface
completed
WP7 highlights 2012 + perspectives 2013
Excel template
Apple and
peach data in
the DB

21. WP7 bioinfoTools
Structure of
phenotypic DB for
apple and peach
completed
Need to
standardize
names
(ontology)
Search tool in
phenotypic
database
User Interface
completed
WP7 highlights 2012 + perspectives 2013
Enter and use
genotypic data
Resequencing data
Excel template
Apple and
peach data in
the DB

22. WP8 Dissemination
WP8 highlights 2012 + perspectives 2013
Design and
management of
the Website
Contacts with stakeholders
(meetings, questionnaires)
1st Newsletter

23. Training
sessions
WP8 Dissemination
WP8 highlights 2012 + perspectives 2013
Design and
management of
the Website
Contacts with stakeholders
(meetings, questionnaires)
1st Newsletter
2nd
Newsletter
Transfer of
technology to
stakeholders